City ended the fourth game in five with 10 men as Sean Geddes became the latest player to receive his marching orders.
After going ahead through Daniel Nti, City failed to clear from a corner with Clayton McDonald heading an own goal on the stroke of half time.
Chorley took an early second half lead before Daniel Nti added his second with a terrific free kick from 25 yards.
With City in the ascendancy Sean Geddes received his second yellow and Chorley took full advantage as substitute Lewis Guy scored with his first touch.
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